BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= 023991
(274 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4GMJ|B Chain B, Structure Of Human Not1 Mif4g Domain Co-Crystallized With
Caf1
pdb|4GMJ|D Chain D, Structure Of Human Not1 Mif4g Domain Co-Crystallized With
Caf1
pdb|4GMJ|F Chain F, Structure Of Human Not1 Mif4g Domain Co-Crystallized With
Caf1
Length = 285
Score = 292 bits (748), Expect = 1e-79, Method: Compositional matrix adjust.
Identities = 143/269 (53%), Positives = 195/269 (72%), Gaps = 12/269 (4%)
Query: 9 SIQIREVWSDNLELEFDLIRKIVDDYPYVAMDTEFPGIALRPVGSFKSSYEYHYQTLKSN 68
S +I EVW+ NL+ E IR+++ Y YVAMDTEFPG+ RP+G F+S+ +Y YQ L+ N
Sbjct: 9 SQRICEVWACNLDEEMKKIRQVIRKYNYVAMDTEFPGVVARPIGEFRSNADYQYQLLRCN 68
Query: 69 VDMLKLIQLGLTFSDENGNLPTCGTDKYCVWQFNFREFDVNEDIFANDSIELLKQSGINF 128
VD+LK+IQLGLTF +E G P GT WQFNF+ F++ ED++A DSIELL SGI F
Sbjct: 69 VDLLKIIQLGLTFMNEQGEYPP-GTS---TWQFNFK-FNLTEDMYAQDSIELLTTSGIQF 123
Query: 129 TKNNEIGIDAMRFGEFMMSSGIVLSDSMHWVTFHSGYDFGYLLKLLTCQNLPDTQVEFFN 188
K+ E GI+ F E +M+SG+VL + + W++FHSGYDFGYL+K+LT NLP+ +++FF
Sbjct: 124 KKHEEEGIETQYFAELLMTSGVVLCEGVKWLSFHSGYDFGYLIKILTNSNLPEEELDFFE 183
Query: 189 LIRIYFPTVYDIKHLMKFCNSLHGGLNKLAELLEVERVGICHQAGSDSLLTASTFRKLKE 248
++R++FP +YD+K+LMK C +L GGL ++AE LE+ER+G HQAGSDSLLT F K++E
Sbjct: 184 ILRLFFPVIYDVKYLMKSCKNLKGGLQEVAEQLELERIGPQHQAGSDSLLTGMAFFKMRE 243
Query: 249 NFFSSSLE--KYAGVLYGLG-----VENG 270
FF ++ KY G LYGLG V+NG
Sbjct: 244 MFFEDHIDDAKYCGHLYGLGSGSSYVQNG 272
>pdb|2D5R|A Chain A, Crystal Structure Of A Tob-Hcaf1 Complex
Length = 252
Score = 288 bits (737), Expect = 3e-78, Method: Compositional matrix adjust.
Identities = 138/257 (53%), Positives = 189/257 (73%), Gaps = 7/257 (2%)
Query: 11 QIREVWSDNLELEFDLIRKIVDDYPYVAMDTEFPGIALRPVGSFKSSYEYHYQTLKSNVD 70
+I EVW+ NL+ E IR+++ Y YVAMDTEFPG+ RP+G F+S+ +Y YQ L+ NVD
Sbjct: 1 RICEVWACNLDEEMKKIRQVIRKYNYVAMDTEFPGVVARPIGEFRSNADYQYQLLRCNVD 60
Query: 71 MLKLIQLGLTFSDENGNLPTCGTDKYCVWQFNFREFDVNEDIFANDSIELLKQSGINFTK 130
+LK+IQLGLTF +E G P GT WQFNF+ F++ ED++A DSIELL SGI F K
Sbjct: 61 LLKIIQLGLTFMNEQGEYPP-GTS---TWQFNFK-FNLTEDMYAQDSIELLTTSGIQFKK 115
Query: 131 NNEIGIDAMRFGEFMMSSGIVLSDSMHWVTFHSGYDFGYLLKLLTCQNLPDTQVEFFNLI 190
+ E GI+ F E +M+SG+VL + + W++FHSGYDFGYL+K+LT NLP+ +++FF ++
Sbjct: 116 HEEEGIETQYFAELLMTSGVVLCEGVKWLSFHSGYDFGYLIKILTNSNLPEEELDFFEIL 175
Query: 191 RIYFPTVYDIKHLMKFCNSLHGGLNKLAELLEVERVGICHQAGSDSLLTASTFRKLKENF 250
R++FP +YD+K+LMK C +L GGL ++AE LE+ER+G HQAGSDSLLT F K++E F
Sbjct: 176 RLFFPVIYDVKYLMKSCKNLKGGLQEVAEQLELERIGPQHQAGSDSLLTGMAFFKMREMF 235
Query: 251 FSSSLE--KYAGVLYGL 265
F ++ KY G LYGL
Sbjct: 236 FEDHIDDAKYCGHLYGL 252
>pdb|2P51|A Chain A, Crystal Structure Of The S. Pombe Pop2p Deadenylation
Subunit
pdb|3G0Z|A Chain A, Structure Of S. Pombe Pop2p - Zn2+ And Mn2+ Bound Form
pdb|3G10|A Chain A, Structure Of S. Pombe Pop2p - Mg2+ And Mn2+ Bound Form
Length = 333
Score = 266 bits (681), Expect = 8e-72, Method: Compositional matrix adjust.
Identities = 128/256 (50%), Positives = 180/256 (70%), Gaps = 6/256 (2%)
Query: 12 IREVWSDNLELEFDLIRKIVDDYPYVAMDTEFPGIALRPVGSFKSSYEYHYQTLKSNVDM 71
IR+VWS NL+ E +LI +++ YP V+MDTEFPG+ RP+G FKSS +YHYQTL++NVD
Sbjct: 23 IRDVWSTNLQQEMNLIMSLIERYPVVSMDTEFPGVVARPLGVFKSSDDYHYQTLRANVDS 82
Query: 72 LKLIQLGLTFSDENGNLPTCGTDKYCVWQFNFREFDVNEDIFANDSIELLKQSGINFTKN 131
LK+IQ+GL SDE GN P + C WQFNF F++ +D++A +SIELL +SGI+F K+
Sbjct: 83 LKIIQIGLALSDEEGNAPV----EACTWQFNF-TFNLQDDMYAPESIELLTKSGIDFKKH 137
Query: 132 NEIGIDAMRFGEFMMSSGIVLSDSMHWVTFHSGYDFGYLLKLLTCQNLPDTQVEFFNLIR 191
E+GI+ F E ++ SG+VL + + W+TFHSGYDF YLLK +T LP EF+ ++
Sbjct: 138 QEVGIEPADFAELLIGSGLVLQEEVTWITFHSGYDFAYLLKAMTQIPLPAEYEEFYKILC 197
Query: 192 IYFPTVYDIKHLMKFCNSLHGGLNKLAELLEVERVGICHQAGSDSLLTASTFRKLKENFF 251
IYFP YDIK++MK + GL +A+ L++ R+G HQAGSD+LLTA F +++ +F
Sbjct: 198 IYFPKNYDIKYIMKSVLNNSKGLQDIADDLQIHRIGPQHQAGSDALLTARIFFEIRSRYF 257
Query: 252 SSSLE-KYAGVLYGLG 266
S++ + LYGLG
Sbjct: 258 DGSIDSRMLNQLYGLG 273
>pdb|4B8A|B Chain B, Structure Of Yeast Not1 Mif4g Domain Co-Crystallized With
Caf1
Length = 286
Score = 200 bits (508), Expect = 7e-52, Method: Compositional matrix adjust.
Identities = 107/283 (37%), Positives = 161/283 (56%), Gaps = 24/283 (8%)
Query: 3 LLPKGDSIQIREVWSDNLELEFDLIRKIVDDYPYVAMDTEFPGIALRPVGSFKSSYEYHY 62
LP + + +R+VW NL EF +IR++V Y +V++ TEF G RP+G+F+S +YHY
Sbjct: 4 FLPPPNYLFVRDVWKSNLYSEFAVIRQLVSQYNHVSISTEFVGTLARPIGTFRSKVDYHY 63
Query: 63 QTLKSNVDMLKLIQLGLTFSDENGNLPTCGTDKYCVWQFNFREFDVNEDIFANDSIELLK 122
QT+++NVD L IQLGL+ SD NGN P G WQFNF EFD ++I + +S+ELL+
Sbjct: 64 QTMRANVDFLNPIQLGLSLSDANGNKPDNGP---STWQFNF-EFDPKKEIMSTESLELLR 119
Query: 123 QSGINFTKNNEIGIDAMRFGEFMMSSGIVLSDSMHWVTFHSGYDFGYLLKLLTCQNLPDT 182
+SGINF K+ +GID F + +M SG+++ DS+ W+T+H+ YD G+L+ +L ++P+
Sbjct: 120 KSGINFEKHENLGIDVFEFSQLLMDSGLMMDDSVTWITYHAAYDLGFLINILMNDSMPNN 179
Query: 183 QVEFFNLIRIYFPTVYDIKHLMKFCNSLHG---------------GLNKLAELLEVERVG 227
+ +F + Y P YD+ + K L LA+ L + R
Sbjct: 180 KEDFEWWVHQYMPNFYDLNLVYKIIQEFKNPQLQQSSQQQQQQQYSLTTLADELGLPRFS 239
Query: 228 ICHQAGSDSLLTASTF---RKLKENFFS--SSLEKYAGVLYGL 265
I G SLL +F KL + F + KY GV+YG+
Sbjct: 240 IFTTTGGQSLLMLLSFCQLSKLSMHKFPNGTDFAKYQGVIYGI 282
>pdb|4B8C|A Chain A, Nuclease Module Of The Yeast Ccr4-Not Complex
pdb|4B8C|C Chain C, Nuclease Module Of The Yeast Ccr4-Not Complex
pdb|4B8C|E Chain E, Nuclease Module Of The Yeast Ccr4-Not Complex
pdb|4B8C|F Chain F, Nuclease Module Of The Yeast Ccr4-Not Complex
Length = 288
Score = 200 bits (508), Expect = 8e-52, Method: Compositional matrix adjust.
Identities = 107/283 (37%), Positives = 161/283 (56%), Gaps = 24/283 (8%)
Query: 3 LLPKGDSIQIREVWSDNLELEFDLIRKIVDDYPYVAMDTEFPGIALRPVGSFKSSYEYHY 62
LP + + +R+VW NL EF +IR++V Y +V++ TEF G RP+G+F+S +YHY
Sbjct: 6 FLPPPNYLFVRDVWKSNLYSEFAVIRQLVSQYNHVSISTEFVGTLARPIGTFRSKVDYHY 65
Query: 63 QTLKSNVDMLKLIQLGLTFSDENGNLPTCGTDKYCVWQFNFREFDVNEDIFANDSIELLK 122
QT+++NVD L IQLGL+ SD NGN P G WQFNF EFD ++I + +S+ELL+
Sbjct: 66 QTMRANVDFLNPIQLGLSLSDANGNKPDNGP---STWQFNF-EFDPKKEIMSTESLELLR 121
Query: 123 QSGINFTKNNEIGIDAMRFGEFMMSSGIVLSDSMHWVTFHSGYDFGYLLKLLTCQNLPDT 182
+SGINF K+ +GID F + +M SG+++ DS+ W+T+H+ YD G+L+ +L ++P+
Sbjct: 122 KSGINFEKHENLGIDVFEFSQLLMDSGLMMDDSVTWITYHAAYDLGFLINILMNDSMPNN 181
Query: 183 QVEFFNLIRIYFPTVYDIKHLMKFCNSLHG---------------GLNKLAELLEVERVG 227
+ +F + Y P YD+ + K L LA+ L + R
Sbjct: 182 KEDFEWWVHQYMPNFYDLNLVYKIIQEFKNPQLQQSSQQQQQQQYSLTTLADELGLPRFS 241
Query: 228 ICHQAGSDSLLTASTF---RKLKENFFS--SSLEKYAGVLYGL 265
I G SLL +F KL + F + KY GV+YG+
Sbjct: 242 IFTTTGGQSLLMLLSFCQLSKLSMHKFPNGTDFAKYQGVIYGI 284
>pdb|1UOC|A Chain A, X-Ray Structure Of The Rnase Domain Of The Yeast Pop2
Protein
pdb|1UOC|B Chain B, X-Ray Structure Of The Rnase Domain Of The Yeast Pop2
Protein
Length = 289
Score = 200 bits (508), Expect = 8e-52, Method: Compositional matrix adjust.
Identities = 107/283 (37%), Positives = 161/283 (56%), Gaps = 24/283 (8%)
Query: 3 LLPKGDSIQIREVWSDNLELEFDLIRKIVDDYPYVAMDTEFPGIALRPVGSFKSSYEYHY 62
LP + + +R+VW NL EF +IR++V Y +V++ TEF G RP+G+F+S +YHY
Sbjct: 7 FLPPPNYLFVRDVWKSNLYSEFAVIRQLVSQYNHVSISTEFVGTLARPIGTFRSKVDYHY 66
Query: 63 QTLKSNVDMLKLIQLGLTFSDENGNLPTCGTDKYCVWQFNFREFDVNEDIFANDSIELLK 122
QT+++NVD L IQLGL+ SD NGN P G WQFNF EFD ++I + +S+ELL+
Sbjct: 67 QTMRANVDFLNPIQLGLSLSDANGNKPDNGP---STWQFNF-EFDPKKEIMSTESLELLR 122
Query: 123 QSGINFTKNNEIGIDAMRFGEFMMSSGIVLSDSMHWVTFHSGYDFGYLLKLLTCQNLPDT 182
+SGINF K+ +GID F + +M SG+++ DS+ W+T+H+ YD G+L+ +L ++P+
Sbjct: 123 KSGINFEKHENLGIDVFEFSQLLMDSGLMMDDSVTWITYHAAYDLGFLINILMNDSMPNN 182
Query: 183 QVEFFNLIRIYFPTVYDIKHLMKFCNSLHG---------------GLNKLAELLEVERVG 227
+ +F + Y P YD+ + K L LA+ L + R
Sbjct: 183 KEDFEWWVHQYMPNFYDLNLVYKIIQEFKNPQLQQSSQQQQQQQYSLTTLADELGLPRFS 242
Query: 228 ICHQAGSDSLLTASTF---RKLKENFFS--SSLEKYAGVLYGL 265
I G SLL +F KL + F + KY GV+YG+
Sbjct: 243 IFTTTGGQSLLMLLSFCQLSKLSMHKFPNGTDFAKYQGVIYGI 285
>pdb|2YBX|A Chain A, Crystal Structure Of Human
Phosphatidylinositol-5-Phosphate 4-Kinase Type-2 Alpha
pdb|2YBX|B Chain B, Crystal Structure Of Human
Phosphatidylinositol-5-Phosphate 4-Kinase Type-2 Alpha
Length = 394
Score = 28.9 bits (63), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 17/61 (27%), Positives = 30/61 (49%), Gaps = 6/61 (9%)
Query: 135 GIDAMRFGEFMMSSGIVLSDSMHW--VTFHSGYDFGYLLKLLTCQNLPDTQVEFFNLIRI 192
GID F + S + +DS FH+ YD Y++K +T +++ E N+++
Sbjct: 95 GIDDQDFQNSLTRSAPLPNDSQARSGARFHTSYDKRYIIKTITSEDV----AEMHNILKK 150
Query: 193 Y 193
Y
Sbjct: 151 Y 151
>pdb|2O4V|A Chain A, An Arginine Ladder In Oprp Mediates Phosphate Specific
Transfer Across The Outer Membrane
pdb|2O4V|B Chain B, An Arginine Ladder In Oprp Mediates Phosphate Specific
Transfer Across The Outer Membrane
pdb|2O4V|C Chain C, An Arginine Ladder In Oprp Mediates Phosphate Specific
Transfer Across The Outer Membrane
Length = 411
Score = 28.5 bits (62), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 17/69 (24%), Positives = 33/69 (47%), Gaps = 5/69 (7%)
Query: 92 GTDKYCVWQFNFREFDVNEDIFANDSIELLKQSGINFTKNNEIGIDAMRFGEFMMSSGIV 151
G Y W++ +D++ ++ NDS ++ + +T N + ++FG F G+
Sbjct: 66 GGTAYRDWKYQI-NYDLSRNV-GNDSAGYFDEASVTYTGFNPVN---LKFGRFYTDFGLE 120
Query: 152 LSDSMHWVT 160
+ S WVT
Sbjct: 121 KATSSKWVT 129
>pdb|3D45|A Chain A, Crystal Structure Of Mouse Parn In Complex With M7gpppg
pdb|3D45|B Chain B, Crystal Structure Of Mouse Parn In Complex With M7gpppg
Length = 507
Score = 28.5 bits (62), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 34/131 (25%), Positives = 57/131 (43%), Gaps = 21/131 (16%)
Query: 14 EVWSDNLELEFDLIRKIVDDYPYVAMDTEFPGIALRP-VGSFKSSY---EYHYQTLKSNV 69
E+ N ++ + + +++ + A+D EF GI+ P V + S + E YQ LK +
Sbjct: 4 EIIRSNFKINLHKVYQAIEEADFFAIDGEFSGISDGPSVTALTSGFDTPEERYQKLKKHS 63
Query: 70 DMLKLIQLGL-TFSDENGNLPTCGTDKYCVWQFNFREF---------DVNEDIFANDSIE 119
L Q GL F ++ + K+ FNF F DV + + + SI+
Sbjct: 64 MDFLLFQFGLCAFKYDHTD------SKHVTKSFNFYVFPKPFSRSSPDV-KFVCQSSSID 116
Query: 120 LLKQSGINFTK 130
L G +F K
Sbjct: 117 FLASQGFDFNK 127
>pdb|2A1R|A Chain A, Crystal Structure Of Parn Nuclease Domain
pdb|2A1R|B Chain B, Crystal Structure Of Parn Nuclease Domain
pdb|2A1S|A Chain A, Crystal Structure Of Native Parn Nuclease Domain
pdb|2A1S|B Chain B, Crystal Structure Of Native Parn Nuclease Domain
pdb|2A1S|C Chain C, Crystal Structure Of Native Parn Nuclease Domain
pdb|2A1S|D Chain D, Crystal Structure Of Native Parn Nuclease Domain
Length = 430
Score = 28.1 bits (61), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 35/136 (25%), Positives = 58/136 (42%), Gaps = 19/136 (13%)
Query: 14 EVWSDNLELEFDLIRKIVDDYPYVAMDTEFPGIALRP-VGSFKSSY---EYHYQTLKSNV 69
E+ N + + + +++ + A+D EF GI+ P V + + + E YQ LK +
Sbjct: 2 EIIRSNFKSNLHKVYQAIEEADFFAIDGEFSGISDGPSVSALTNGFDTPEERYQKLKKHS 61
Query: 70 DMLKLIQLGL-TFSDENGNLPTCGTDKYCVWQFNF----REFDVNED----IFANDSIEL 120
L Q GL TF + + KY FNF + F+ + + + SI+
Sbjct: 62 MDFLLFQFGLCTFKYDYTD------SKYITKSFNFYVFPKPFNRSSPDVKFVCQSSSIDF 115
Query: 121 LKQSGINFTKNNEIGI 136
L G +F K GI
Sbjct: 116 LASQGFDFNKVFRNGI 131
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.322 0.139 0.420
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,647,470
Number of Sequences: 62578
Number of extensions: 372454
Number of successful extensions: 794
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 780
Number of HSP's gapped (non-prelim): 11
length of query: 274
length of database: 14,973,337
effective HSP length: 97
effective length of query: 177
effective length of database: 8,903,271
effective search space: 1575878967
effective search space used: 1575878967
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 51 (24.3 bits)